+Open data
-Basic information
Entry | Database: PDB / ID: 4pe5 | |||||||||||||||
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Title | Crystal Structure of GluN1a/GluN2B NMDA Receptor Ion Channel | |||||||||||||||
Components | (Glutamate receptor ionotropic, NMDA ...) x 2 | |||||||||||||||
Keywords | TRANSPORT PROTEIN / NMDA receptor / GluN1 / GluN2B / ion channel | |||||||||||||||
Function / homology | Function and homology information neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / regulation of postsynaptic cytosolic calcium ion concentration / NMDA selective glutamate receptor signaling pathway / sensory organ development / sensitization / fear response / pons maturation ...neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / regulation of postsynaptic cytosolic calcium ion concentration / NMDA selective glutamate receptor signaling pathway / sensory organ development / sensitization / fear response / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / olfactory learning / conditioned taste aversion / regulation of protein kinase A signaling / protein localization to postsynaptic membrane / apical dendrite / dendritic branch / regulation of respiratory gaseous exchange / propylene metabolic process / response to glycine / response to other organism / response to methylmercury / voltage-gated monoatomic cation channel activity / response to morphine / glutamate-gated calcium ion channel activity / positive regulation of cysteine-type endopeptidase activity / cellular response to dsRNA / regulation of monoatomic cation transmembrane transport / response to carbohydrate / interleukin-1 receptor binding / negative regulation of dendritic spine maintenance / cellular response to lipid / positive regulation of glutamate secretion / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / RAF/MAP kinase cascade / response to growth hormone / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / calcium ion transmembrane import into cytosol / protein heterotetramerization / response to manganese ion / glutamate binding / positive regulation of reactive oxygen species biosynthetic process / neuromuscular process / startle response / regulation of synapse assembly / action potential / glycine binding / positive regulation of calcium ion transport into cytosol / regulation of neuronal synaptic plasticity / male mating behavior / regulation of dendrite morphogenesis / regulation of axonogenesis / receptor clustering / heterocyclic compound binding / suckling behavior / behavioral response to pain / monoatomic cation transmembrane transport / response to amine / social behavior / small molecule binding / ligand-gated monoatomic ion channel activity / monoatomic cation transport / positive regulation of excitatory postsynaptic potential / regulation of MAPK cascade / response to magnesium ion / associative learning / excitatory synapse / behavioral fear response / positive regulation of dendritic spine maintenance / extracellularly glutamate-gated ion channel activity / multicellular organismal response to stress / cellular response to organic cyclic compound / Unblocking of NMDA receptors, glutamate binding and activation / long-term memory / regulation of postsynaptic membrane potential / glutamate receptor binding / D2 dopamine receptor binding / phosphatase binding / calcium ion homeostasis / synaptic cleft / cellular response to manganese ion / prepulse inhibition / positive regulation of synaptic transmission / detection of mechanical stimulus involved in sensory perception of pain / response to mechanical stimulus / response to electrical stimulus / regulation of neuron apoptotic process / presynaptic active zone membrane / cellular response to forskolin / response to amphetamine / response to fungicide / monoatomic cation channel activity / glutamate-gated receptor activity / sensory perception of pain Similarity search - Function | |||||||||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.96 Å | |||||||||||||||
Authors | Karakas, E. / Furukawa, H. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Science / Year: 2014 Title: Crystal structure of a heterotetrameric NMDA receptor ion channel. Authors: Karakas, E. / Furukawa, H. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pe5.cif.gz | 564.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pe5.ent.gz | 427.4 KB | Display | PDB format |
PDBx/mmJSON format | 4pe5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/4pe5 ftp://data.pdbj.org/pub/pdb/validation_reports/pe/4pe5 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Glutamate receptor ionotropic, NMDA ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 92680.945 Da / Num. of mol.: 2 / Fragment: UNP residues 23-847 Mutation: N61Q, N239D, N350Q, N471Q, N491Q, T561C, E594Q, E595S, E597S, E598T, N771Q, F810C, R844N, R845G, K846A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin1, Nmdar1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35439 #2: Protein | Mass: 92163.352 Da / Num. of mol.: 2 / Fragment: UNP residues 27-852 Mutation: S214C, N348D, D557C, C588S, I815C, C838S, C849S, del(C395), del(P396), del(E397), del(E399), del(E400), del(E402) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2b / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q00960 |
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-Sugars , 5 types, 14 molecules
#3: Polysaccharide | #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #9: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 90 molecules
#7: Chemical | ChemComp-W / #8: Chemical | #10: Chemical | #11: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.2 Å3/Da / Density % sol: 70.69 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: PEG 4000, Tris-HCl, NaCl, Magnesium acetate, metatungstate PH range: 8.0-8.8 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 7, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.95→50 Å / Num. obs: 52241 / % possible obs: 98.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 196.24 Å2 / Rmerge(I) obs: 0.087 / Χ2: 1.348 / Net I/av σ(I): 13.025 / Net I/σ(I): 9.3 / Num. measured all: 197482 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 3QEL, 2A5T Resolution: 3.96→29.717 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.96→29.717 Å
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Refine LS restraints |
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LS refinement shell |
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